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KIDAL, Mali (Reuters) - French and Malian troops are fighting Islamist rebels in the Sahara outside northern Mali's biggest town, France's defence minister said on Wednesday, describing the desert campaign against al Qaeda as a "real war" that was far from won.

After driving the Islamists from northern Mali's main towns with three weeks of air strikes and a lightning ground advance, France is now pursuing them in the remote northeast, where pro-autonomy Tuaregs are pressing their own territorial claims.

French Defence Minister Jean-Yves Le Drian said French and Malian joint patrols were searching the scrubland outside the desert trading towns of Timbuktu and Gao. Gao residents said on Tuesday the town had been hit by rebel rockets fired from the bush.

"There were clashes yesterday at Gao because from the moment where our forces, supported by the Malian forces, started undertaking missions and patrols around the towns we had taken, we encountered Jihadist groups that fought," Le Drian told Europe 1 radio. "It's a real war."

With just 4,000 ground troops in an area the size of Texas, France has appealed for the swift deployment of a U.N.-backed African military force (AFISMA) to help secure the region, and says it expects to start pulling its troops out from March.

The African deployment has been slowed by lack of transport and equipment, but Foreign Minister Laurent Fabius told reporters in Paris that France wanted the African force to be converted into a U.N. peacekeeping force by April.

WORKING WITH TUAREGS

"From the moment that security is assured, we can envisage without changing the structures that it can be placed under the framework of U.N. peacekeeping operations," he said.

France has said that several hundred Islamist fighters have been killed since it intervened In Mali on January 11 to turn back an Islamist column advancing south toward the capital.

With logistical support from Washington and European allies, it wants to restore stability and remove the threat of Islamists using Mali as a base to launch attacks in Africa and the West.

French troops are cooperating with Tuareg pro-autonomy MNLA rebels who say they have occupied the remote northeastern town of Kidal and surrounding areas after the Islamist fighters fled French air strikes into the nearby Adrar des Ifoghas mountains.

But that on-ground cooperation, and France's public insistence that the MNLA should take part in talks on Mali's political future if it drops a demand for full independence for the north, is an irritant for Mali's troubled military.

"The MNLA are playing PR ... they might go and occupy those places where there is nobody and pretend they are militarily present, but they don't represent anything for us," said a Malian military source who asked not to be named.

Mali's armed forces are still smarting from their defeat in last year's northern Tuareg rebellion, which triggered a coup in the capital Bamako and was later hijacked by Islamist jihadists. Many ordinary Malians deeply resent the MNLA for opening the door to the Islamists' seizure of the north.

Interim President Dioncounda Traore, installed by the military after last year's coup, has offered talks to the MNLA if they do not seek full independence, and says he is aiming to hold a national election by July 31.

TUAREGS NOT UNITED

Experts say the MNLA are poorly organised and divided and represent only a part of the north's population.

"There will never, ever be a solution if you don't talk to the Tuaregs - but they are not homogenous," said Jeremy Keenan, a British anthropologist and expert on the Tuaregs.

"You have a huge part of the rest of Mali not wanting to have anything to do with the Tuaregs - the Tuareg problem has to be resolved and it goes wider than Mali." There are also restive Tuareg communities in neighbouring Algeria and Niger.

Paris argues that lasting peace in Mali hinges on political talks to reconcile the black African-dominated government in Bamako with the restive north, in particular the Tuaregs.

Positioning itself for talks, the MNLA said on Tuesday it had occupied the town of Menaka, more than 250 km (185 miles) south of its remote northern stronghold of Kidal.

The MNLA has started its own patrols in the remote regions around the Algerian border where Islamist fighters are believed to be holding seven French citizens hostage. It announced this week it had arrested two senior Islamists fleeing to Algeria.

French special forces and some 1,800 Chadian troops are also based in Kidal, but Malian government troops have kept away.

"AFISMA and also the Malian army will deploy eventually to Kidal," AFISMA spokesman Col. Yao Adjoumani told a news conference in Bamako. "Talks between the MNLA and the government will take place later."